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Determining spatio-temporal distributions of fish populations is of interest to marine ecology, in general, and to fisheries science in particular. Genetic mixed-stock analysis is routinely applied in several anadromous fishes for determining migratory routes and timing but has rarely been used for marine fishes, for which population differentiation is commonly weak and the method presumably less powerful. We used microsatellite information for Northeast Atlantic herring Clupea harengus L. populations and mixed stocks to address 2 questions. We used simulated mixture samples and 3 different statistical approaches to determine whether mixed stock composition could be determined with accuracy. Simulations showed that the applied approaches and mixture samples of 100 individuals enabled detailed composition analyses on a regional level, with resolution for tracing the ecologically dominant Rügen (Greifswalder Bodden) herring population. We then estimated spatio-temporal variation in herring migratory behaviour in the Skagerrak from 17 mixed samples collected over 2 seasons and 2 yr, and identified hitherto undescribed differences in distributions among populations that feed and winter in the area.

Transcriptome studies of insect herbivory are still rare, yet studies in model systems have uncovered patterns of transcript regulation that appear to provide insights into how insect herbivores attain polyphagy, such as a general increase in expression breadth and regulation of ribosomal, digestion- and detoxification-related genes. We investigated the potential generality of these emerging patterns, in the Swedish comma, Polygonia c-album, which is a polyphagous, widely-distributed butterfly. Urtica dioica and Ribes uva-crispa are hosts of P. c-album, but Ribes represents a recent evolutionary shift onto a very divergent host. Utilizing the assembled transcriptome for read mapping, we assessed gene expression finding that caterpillar life-history (i.e. 2nd vs. 4th-instar regulation) had a limited influence on gene expression plasticity. In contrast, differential expression in response to host-plant identified genes encoding serine-type endopeptidases, membrane-associated proteins and transporters. Differential regulation of genes involved in nucleic acid binding was also observed suggesting that polyphagy involves large scale transcriptional changes. Additionally, transcripts coding for structural constituents of the cuticle were differentially expressed in caterpillars in response to their diet indicating that the insect cuticle may be a target for plant defence. Our results state that emerging patterns of transcript regulation from model species appear relevant in species when placed in an evolutionary context.

Census (NC) and effective population size (Ne) were estimated for a lake-resident population of brown trout Salmo trutta as 576 and 63, respectively. The point estimate of the ratio of effective to census population size (Ne:NC) for this population is 0·11 with a range of 0·06–0·26, suggesting that Ne:NC ratio for lake-resident populations agree more with estimates for fishes with anadromous life histories than the small ratios observed in many marine fishes

Background: Although most insect species are specialized on one or few groups of plants, there are phytophagous insects that seem to use virtually any kind of plant as food. Understanding the nature of this ability to feed on a wide repertoire of plants is crucial for the control of pest species and for the elucidation of the macroevolutionary mechanisms of speciation and diversification of insect herbivores. Here we studied Vanessa cardui, the species with the widest diet breadth among butterflies and a potential insect pest, by comparing tissue-specific transcriptomes from caterpillars that were reared on different host plants. We tested whether the similarities of gene-expression response reflect the evolutionary history of adaptation to these plants in the Vanessa and related genera, against the null hypothesis of transcriptional profiles reflecting plant phylogenetic relatedness. Result: Using both unsupervised and supervised methods of data analysis, we found that the tissue-specific patterns of caterpillar gene expression are better explained by the evolutionary history of adaptation of the insects to the plants than by plant phylogeny. Conclusion: Our findings suggest that V. cardui may use two sets of expressed genes to achieve polyphagy, one associated with the ancestral capability to consume Rosids and Asterids, and another allowing the caterpillar to incorporate a wide range of novel host-plants.

Rapid advances in molecular genetic techniques and the statistical analysis of genetic data have revolutionized the way that populations of animals, plants and microorganisms can be monitored. Genetic monitoring is the practice of using molecular genetic markers to track changes in the abundance, diversity or distribution of populations, species or ecosystems over time, and to follow adaptive and non-adaptive genetic responses to changing external conditions. In recent years, genetic monitoring has become a valuable tool in conservation management of biological diversity and ecological analysis, helping to illuminate and define cryptic and poorly understood species and populations. Many of the detected biodiversity declines, changes in distribution and hybridization events have helped to drive changes in policy and management. Because a time series of samples is necessary to detect trends of change in genetic diversity and species composition, archiving is a critical component of genetic monitoring. Here we discuss the collection, development, maintenance, and use of archives for genetic monitoring. This includes an overview of the genetic markers that facilitate effective monitoring, describes how tissue and DNA can be stored, and provides guidelines for proper practice.

The wild wolf population (Canis lupus) in Sweden is classified as Endangered and descends from only five individuals. The population is isolated and highly inbred; individuals are on average more related to each other than siblings. Inbreeding depression expressed as reduced litter size and a high frequency of spinal disorders have been reported. Management goals include reducing levels of inbreeding, and one suggestion to achieve this is through crossfostering release of pups from a zoo conservation breeding program into wild dens. We used pedigree data of the wild and zoo populations, respectively, to evaluate to what extent the zoo population can support the wild one with respect to increased genetic variation and reduction of inbreeding. The results show a potential to almost double genetic variation measured as founder alleles from 11.2 to 21.1, despite the fact that the two populations have three common founders. Potentially, the number of founder genome equivalents can be increased from present 1.8 to around 3.2. However, to achieve maximum genetic support, almost 50 percent of the wild population gene pool must consist of genes from the zoo population. Average kinship in the joint population of zoo and wild wolves is 0.15, thus release of zoo wolves cannot in itself be expected to reduce average inbreeding below the management target of 0.1. We conclude that releases from the zoo can support but not resolve the genetically precarious situation of the wild Swedish wolf population.

7.

Jansson, Mija

et al.

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

Laikre, Linda

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

Increasing conservation genetic focus is directed towards domestic animal populations because: 1) domestic animals are of direct socio-economic importance to humans, and 2) strong selective breeding for a single or a few traits are considered to rapidly deplete the genetic variability of many domestic animal populations. International policy work within the Convention on Biological Diversity identifies strategies for minimizing genetic erosion of domesticated animals as one of the key biodiversity targets for 2010-2020. We investigated recent rate of inbreeding and loss of genetic variation in 12 traditional Swedish dog breeds, 10 of which have been identified as of conservation concern by the Swedish Board of Agriculture. We used studbook data provided by the Swedish Kennel Club with pedigrees dating back to the mid 20th century and comprising 5-10 generations with 350-60,000 individuals per pedigree. We assessed levels of inbreeding and loss of genetic variation measured in relation to the number of founding animals (founder alleles) among live animals at five points in time (1980, 1990, 2000, 2006, and 2012). We found average inbreeding coefficients among breeds to double over our period of monitoring, from an average of 0.03 over breeds in 1980 to 0.07 in 2012. This is in spite of the majority of breeds being large with pedigrees comprising thousands of individuals. The loss of genetic variation is extensive with an average of 70 percent loss of founder alleles over the study period, and the proportion of founder genome equivalents in relation to the number of founders is on average only 0.09. This is comparable to previously published rates of genetic variability loss in dog breeds, indicating that the explicit conservation goals for these traditional Swedish breeds is not yet reflected in conservation genetic status. One of the breeds is particularly threatened - the Gotland hound with less than 150 living individuals, but this breed also shows comparably larger retention of genetic variation.

8.

Jansson, Mija

et al.

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

Laikre, Linda

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

One problem in modern dogs is a high occurrence of physical diseases,defects and disorders. Many breeds exhibit physical problems that affectindividual dogs throughout life. A potential cause of these problems isinbreeding that is known to reduce the viability of individuals. We investigatedthe possible correlation between recent inbreeding and health problemsin dogs and used studbook data from 26 breeds provided by theSwedish Kennel Club for this purpose. The pedigrees date back to themid-20th century and comprise 5–10 generations and 1 000–50 000 individualsper pedigree over our study period of 1980–2010. We comparedlevels of inbreeding and loss of genetic variation measured in relation tothe number of founding animals during this period in the investigated dogbreeds that we classified as ‘healthy’ (11 breeds) or ‘unhealthy’ (15) basedon statistics on the extent of veterinary care obtained from Sweden’sfour largest insurance companies for pets. We found extensive loss ofgenetic variation and moderate levels of recent inbreeding in all breedsexamined, but no strong indication of a difference in these parametersbetween healthy versus unhealthy breeds over this period. Thus, recentbreeding history with respect to rate of inbreeding does not appear to be amain cause of poor health in the investigated dog breeds in Sweden. Weidentified both strengths and weaknesses of the dog pedigree data importantto consider in future work of monitoring and conserving geneticdiversity of dog breeds.

There is a growing need for conservation genetic management of animal populations when individual relatedness data (pedigrees) are available. Such data can be used to monitor rates of inbreeding and loss of genetic diversity. Traditionally, pedigree analysis for conservationmanagement has focused on zoo populations of threatened wild animals; available software has been developed in that context. Population Management x (PMx) is a free software for estimating genetic parameters including inbreeding, kinship, founder allele contribution and survival. PMx is an accessory program to the zoo studbook platform Single Population Analysis and Records Keeping System (SPARKS) and is not easily applied outside this platform, but such use is of interest for various domestic breeds or wild populations. We developed a converter program (mPed) for making pedigrees of any studbook format fitting the input requirements of PMx. mPed can be downloaded free at www.popgen.su.se/mped.php

Most species comprise a number of more or less reproductively isolated subpopulations. These subpopulations may exhibit striking differences in morphology and ecology, and on the basis of those differences they are often given the rank of subspecies, race, stock, variety, etc. Morphological and ecological traits most often are quantitatively inherited, and to a large extent, are affected by environmental factors. Phenotypic differences, therefore, may give little or no information on genotypic differences. As a consequence, the amount of genetic divergence between populations in many cases is poorly known.

The need for such information from an evolutionary and management perspective provided the impetus for this study, which describes the genetical and morphological variability patterns revealed by protein polymorphism and morphological characters. Four species were chosen from three diverse taxonomic groups: Atlantic herring (Clupea harengus), Norway spruce (Picea abies), and Palaemon prawn (P. adspersus and P. squilla). Associations between variability patterns for the two sets of characters were also analyzed to provide information on the causes of morphological variability in natural populations.

In Atlantic herring, the amount of genetic differentiation observed was conspicuously small: more than 99% of the total gene diversity was found within populations. This contrasts with previous conclusions that were based on morphological data. The present study indicates that environmental factors have an important influence on the morphological differentiation pattern; they suggest, also, that herring stocks either diverged rather recently or that the amount of gene flow is large enough to prevent genetic differentiation.

The patterns for distribution of genetical and morphological variability in Norway spruce, on the other hand, are very similar, indicating that the same evolutionary forces have acted on both sets of characters. A clear geographic component of variation was also observed. Data suggest that historical events during the last glaciation have affected not only the pattern of distribution of allozymic variation in the Norway spruce but probably also the pattern of its morphological traits.

The analysis of data collected from progeny of wind-pollinated Norway spruce grown under experimental conditions suggests that inbreeding and inbreeding depression are common phenomena in trials of this species. A significant positive relationship found between allozyme heterozygosity and growth performance (apparent allozyme heterosis) in one population appears to be due to dominance rather than overdominance.

Members of nontidal populations of the prawn Palaemon squilla are known to be much smaller than their tidal relatives, and to produce fewer offspring. Using estimates of genetic divergence based on allozyme data, we tested the hypothesis that these deficiencies are an effect of continuous gene flow resulting in poor adaptation. Genetic data did not support this hypothesis: P. squilla ought to have the possibility to adapt to local conditions.

The results from the present study modify some previous conceptions about genetical and morphological variability patterns in all species that were investigated.

In combination these findings demonstrate the importance of true genetic data for clarifying genetic population structure, understanding the forces that underlie current population structure, and for interpreting ecological and morphological variability patterns among natural populations.

12.

Laikre, Linda

et al.

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

Jansson, Mija

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

The wolf (Canis lupus) is classified as endangered in Sweden by the Swedish Species Information Centre, which is the official authority for threat classification. The present population, which was founded in the early 1980s, descends from 5 individuals. It is isolated and highly inbred, and on average individuals are more related than siblings. Hunts have been used by Swedish authorities during 2010 and 2011 to reduce the population size to its upper tolerable level of 210 wolves. European Union (EU) biodiversity legislation requires all member states to promote a concept called “favourable conservation status” (FCS) for a series of species including the wolf. Swedish national policy stipulates maintenance of viable populations with sufficient levels of genetic variation of all naturally occurring species. Hunting to reduce wolf numbers in Sweden is currently not in line with national and EU policy agreements and will make genetically based FCS criteria less achievable for this species. We suggest that to reach FCS for the wolf in Sweden the following criteria need to be met: (1) a well-connected, large, subdivided wolf population over Scandinavia, Finland, and the Russian Karelia-Kola region should be reestablished, (2) genetically effective size (Ne) of this population is in the minimum range of Ne = 500–1000, (3) Sweden harbors a part of this total population that substantially contributes to the total Ne and that is large enough to not be classified as threatened genetically or according to IUCN criteria, and (4) average inbreeding levels in the Swedish population are <0.1.

The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Åland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran’s I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100–150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.

Introduction of alien species is a major threat to biological diversity. Although public attention typically focuses on the species level, guidelines from the Convention of Biological Diversity define alien species to include entities below species level. This inclusion recognizes that release of nonlocal populations of native species may also result in negative effects on biodiversity. In practice, little is known about the extent, degree of establishment, or the effects on natural gene pools of such releases. Existing information on the releases in Sweden shows that alien populations are spread to a great extent. The most commonly released species include brown trout, Atlantic salmon, Arctic char, common whitefish, Scots pine, Norway spruce, mallard duck, gray partridge, and pheasant. Although millions of forest trees, fish, and birds are released annually, poor documentation makes the geographic and genetic origin of these populations, as well as the sites where they have been released, largely unclear. We provide recommendations for urgently needed first steps relating to the risks and problems associated with release of alien populations.

15.

Larsson, Lena C.

et al.

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

Laikre, Linda

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

André, Carl

Tjärnö marinbiologiska laboratorium, Göteborgs universitet.

Dahlgren, Thomas G.

Göteborgs universitet.

Ryman, Nils

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

Information on the temporal stability of genetic structures is important to permit detection of changes that can constitute threats to biological resources. Large scale harvesting operations are known to potentially alter the composition and reduce the variability of populations, and Atlantic herring (Clupea harengus) has a long history of heavy exploitation. In the Baltic Sea and Skagerrak waters the census population sizes have declined by 35-50% over the last three decades. We compared the genetic structure of Atlantic herring in these waters sampled at least two different times between 1979 and 2003 by assaying eleven allozyme and nine microsatellite loci. We cannot detect any changes in the amount of genetic variation or spatial structure, and differentiation is weak with overall FST=0.003 among localities for the older samples and FST=0.002 for the newer ones. There are indications of temporal allele frequency changes, particularly in one of five sampling localities that is reflected in a relatively small local Ne estimate of c. 400. The previously identified influence of selection at the microsatellite locus Cpa112 remains stable over the 24-year period studied here. In spite of little genetic differentiation, migration among localities appears small enough to permit demographic independence between populations.

Population census size (NC) and effective population sizes (Ne) are two crucial parameters that influence population viability, wildlife management decisions, and conservation planning. Genetic estimators of both NC and Ne are increasingly widely used because molecular markers are increasingly available, statistical methods are improving rapidly, and genetic estimators complement or improve upon traditional demographic estimators. We review the kinds and applications of estimators of both NC and Ne, and the often undervalued and misunderstood ratio of effective-to-census size (Ne/NC). We focus on recently improved and well evaluated methods that are most likely to facilitate conservation. Finally, we outline areas of future research to improve Ne and NC estimation in wild populations

In this study, the genetic variation of perch Perca fluviatilis from 18 different sites along the Swedish coast of the Baltic Sea was assessed. There was a relative strong support for isolation by distance and the results suggest an overall departure from panmixia. The level of genetic divergence was moderate (global FST = 0·04) and indications of differences in the population genetic structure between the two major basins (central Baltic Sea and Gulf of Bothnia) in the Baltic Sea were found. There was a higher level of differentiation in the central Baltic Sea compared to the Gulf of Bothnia, and the results suggest that stretches of deep water might act as barriers to gene flow in the species. On the basis of the estimation of genetic patch size, the results corroborate previous mark–recapture studies and suggest that this is a species suitable for local management. In all, the findings of this study emphasize the importance of considering regional differences even when strong isolation by distance characterize the genetic population structure of species.

Detecting population subdivision when apparent barriers to gene flow are lacking is important in evolutionary and conservation biology. Recent research indicates that intraspecific population complexity can be crucial for maintaining a species' evolutionary potential, productivity, and ecological role. We monitored the genetic relationships at 14 allozyme loci among similar to 4,000 brown trout (Salmo trutta) collected during 19 years from two small interconnected mountain lakes (0.10 and 0.17 km(2), respectively) in central Sweden. There were no allele frequency differences between the lakes. However, heterozygote deficiencies within lakes became obvious after a few years of monitoring. Detailed analyses were then carried out without a priori grouping of samples, revealing unexpected differentiation patterns: (i) the same two genetically distinct (F (ST) a parts per thousand yen 0.10) populations occur sympatrically at about equal frequencies within both lakes, (ii) the genetic subdivision is not coupled with apparent phenotypical dichotomies, (iii) this cryptic structure remains stable over the two decades monitored, and (iv) the point estimates of effective population size are c. 120 and 190, respectively, indicating that genetic drift is important in this system. A subsample of 382 fish was also analyzed for seven microsatellites. The genetic pattern does not follow that of the allozymes, and in this subsample the presence of multiple populations would have gone undetected if only scoring microsatellites. Sympatric populations may be more common than anticipated, but difficult to detect when individuals cannot be grouped appropriately, or when markers or sample sizes are insufficient to provide adequate statistical power with approaches not requiring prior grouping.

It is contentious to what extent sympatric speciation represents a general and taxonomically widespread phenomenon. Documenting the occurrence of multiple, genetically distinct populations within areas lacking barriers to gene flow can increase our understanding of this type of speciation, because such populations are expected to represent the first steps of sympatric speciation. We analyzed the genetic relationships among over 4000 brown trout (Salmo trutta) collected during 19 sampling years from a series of small mountain lakes in northern Scandinavia. Our results clearly indicate the presence of two sympatric populations within these lakes. The populations are characterized by a high degree of genetic divergence coupled with a lack of apparent phenotypic dichotomy. The differentiation pattern appears stable over the two decades monitored, and the exchange of individuals between the two populations appears small. The existence of sympatric populations characterized by substantial genetic divergence may be a much more common phenomenon than anticipated, but difficult to detect in situations where morphological or ecological differentiation is missing. Larger samples than typically collected in a single sampling effort may be needed for revealing situations of sympatry, and for reliable estimation of the number of populations.

20.

Palmé, Anna

et al.

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

Wennerström, Lovisa

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.

Guban, Peter

Laikre, Linda

Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.